Sodium in PDB 3e8l: The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

Enzymatic activity of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

All present enzymatic activity of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins:
3.4.21.4;

Protein crystallography data

The structure of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins, PDB code: 3e8l was solved by R.Bao, C.-H.Jiang, C.W.Chi, S.X.Lin, Y.X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 2.48
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	76.634, 110.863, 152.991, 90.00, 90.00, 90.00
*R / R_free (%)*	19.4 / 24.5

Other elements in 3e8l:

The structure of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins (pdb code 3e8l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins, PDB code: 3e8l:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3e8l

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Sodium Binding Sites List in 3e8l

Sodium binding site 1 out of 3 in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1 b:43.2 occ:1.00	N	A:THR122	3.0	38.5	1.0
	OG1	A:THR122	3.2	39.9	1.0
	O	A:HOH293	3.2	43.4	1.0
	N	A:SER123	3.5	40.0	1.0
	O	A:SER123	3.5	40.0	1.0
	CG	A:LYS201	3.6	37.9	1.0
	NE2	A:GLN203	3.7	39.2	1.0
	CA	A:PRO121	3.8	38.6	1.0
	CA	A:THR122	3.9	39.1	1.0
	C	A:PRO121	3.9	38.7	1.0
	OG	A:SER123	3.9	41.3	1.0
	CE	A:LYS201	4.0	38.5	1.0
	CB	A:PRO121	4.0	38.6	1.0
	C	A:THR122	4.0	39.6	1.0
	CD	A:LYS201	4.1	36.8	1.0
	CB	A:THR122	4.1	39.1	1.0
	CB	A:LYS201	4.2	38.0	1.0
	C	A:SER123	4.3	40.2	1.0
	CA	A:SER123	4.4	40.1	1.0
	O	A:HOH275	4.6	44.1	1.0
	CB	A:SER123	4.7	40.0	1.0
	CG2	A:THR122	4.9	38.6	1.0
	CD	A:GLN203	5.0	38.2	1.0

Sodium binding site 2 out of 3 in 3e8l

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Sodium Binding Sites List in 3e8l

Sodium binding site 2 out of 3 in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na3 b:35.0 occ:0.80	OE1	A:GLN170	2.9	43.8	1.0
	O	A:HOH289	2.9	31.2	1.0
	OG	A:SER210	3.0	37.9	0.5
	O	A:HOH250	3.0	29.6	1.0
	CD	A:GLN170	3.7	41.7	1.0
	CE2	C:PHE143	3.8	27.1	1.0
	NE2	A:GLN170	3.8	39.4	1.0
	CH3	C:ACT181	3.8	35.0	0.8
	CZ	C:PHE143	3.9	27.1	1.0
	CD1	A:TYR167	3.9	34.2	1.0
	OG1	C:THR66	4.0	27.1	1.0
	CE1	A:TYR167	4.3	34.2	1.0
	CB	A:SER210	4.4	37.8	0.5
	CB	A:SER210	4.4	37.6	0.5
	CD2	C:PHE143	4.4	26.2	1.0
	CE1	C:PHE143	4.6	25.7	1.0
	O1	A:GOL2	4.6	35.0	0.8
	OG	A:SER210	4.7	36.6	0.5
	CZ3	A:TRP208	4.7	36.0	1.0
	C	C:ACT181	4.9	35.0	0.8

Sodium binding site 3 out of 3 in 3e8l

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Sodium Binding Sites List in 3e8l

Sodium binding site 3 out of 3 in the The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of the Double-Headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na7 b:45.5 occ:1.00	CH3	A:ACT6	1.6	35.0	0.8
	O	A:HIS38	2.7	37.8	1.0
	C	A:ACT6	3.1	35.0	0.8
	C	A:HIS38	3.8	37.4	1.0
	OXT	A:ACT6	3.8	35.0	0.8
	CB	A:HIS38	3.9	38.2	1.0
	CD1	A:TYR146	3.9	47.0	1.0
	O	A:ACT6	4.0	35.0	0.8
	CB	C:ALA147	4.1	22.5	1.0
	O	A:HOH269	4.1	30.2	1.0
	CA	A:HIS38	4.3	38.2	1.0
	CD1	A:TYR37	4.3	42.8	1.0
	CE1	A:TYR146	4.4	48.4	1.0
	N	A:HIS38	4.5	38.8	1.0
	CG	A:TYR146	4.5	46.2	1.0
	O	A:TRP136	4.7	38.3	1.0
	N	A:PHE39	4.8	36.6	1.0
	CB	A:TYR146	4.8	45.0	1.0
	CE1	A:TYR37	4.9	44.5	1.0

Reference:

R.Bao, C.Z.Zhou, C.-H.Jiang, S.X.Lin, C.W.Chi, Y.X.Chen. The Ternary Structure of Double-Headed Arrowhead Protease Inhibitor Api-A Complexed with Two Trypsins Reveals A Novel Reactive Site Conformation. J.Biol.Chem. V. 284 26676 2009.
ISSN: ISSN 0021-9258
PubMed: 19640842
DOI: 10.1074/JBC.M109.022095

Page generated: Mon Oct 7 08:49:18 2024

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